13-19935063-A-G

Position:

• chr13-19935063-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430584.1(ZMYM2):​c.-163-15828A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,846 control chromosomes in the GnomAD database, including 14,386 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14386 hom., cov: 32)
• Consequence: ZMYM2 XM_047430584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

ZMYM2 (HGNC:12989): (zinc finger MYM-type containing 2) The protein encoded by this gene is a zinc finger protein that may act as a transcription factor. The encoded protein may be part of a BHC histone deacetylase complex. Translocation of this gene with the fibroblast growth factor receptor-1 gene (FGFR1) results in a fusion gene, which may be a cause of stem cell leukemia lymphoma syndrome (SCLL). Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMYM2	XM_047430584.1	c.-163-15828A>G		intron_variant			XP_047286540.1
ZMYM2	XM_047430585.1	c.-52-17976A>G		intron_variant			XP_047286541.1
		n.19935063A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65724 AN: 151728 Hom.: 14377 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.426

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.433 AC: 65749 AN: 151846 Hom.: 14386 Cov.: 32 AF XY: 0.431 AC XY: 31982 AN XY: 74194

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.423

Alfa AF: 0.405 Hom.: 16413

Bravo AF: 0.442

Asia WGS AF: 0.355 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7320671; hg19: chr13-20509203;